LOCUS       NZ_CP046290             2557 bp    DNA     linear   CON 09-JUL-2023
DEFINITION  Shigella sonnei strain FDAARGOS_715 plasmid unnamed5.
ACCESSION   NZ_CP046290
VERSION     NZ_CP046290.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11056430
            Assembly: GCF_009729995.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2557)
  AUTHORS   Fashae,K., Tallon,L., Sadzewicz,L., Vavikolanu,K., Mehta,A.,
            Aluvathingal,J., Nadendla,S., Nandy,P., Geyer,C., Yan,Y. and
            Sichtig,H.
  TITLE     FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS):
            Supporting development and validation of Infectious Disease Dx tests
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2557)
  AUTHORS   Fashae,K., Tallon,L., Sadzewicz,L., Vavikolanu,K., Mehta,A.,
            Aluvathingal,J., Nadendla,S., Nandy,P., Geyer,C., Yan,Y. and
            Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-NOV-2019) Center for Devices and Radiological Health,
            US Food and Drug Administration, 10903 New Hampshire Avenue, Silver
            Spring, MD 20993-0002, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SMRT v. 2.3.0, HGAP v. 3
            Genome Coverage                   :: 521.02x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/09/2023 03:33:55
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,196
            CDSs (total)                      :: 5,069
            Genes (coding)                    :: 4,349
            CDSs (with protein)               :: 4,349
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 720
            CDSs (without protein)            :: 720
            Pseudo Genes (ambiguous residues) :: 0 of 720
            Pseudo Genes (frameshifted)       :: 217 of 720
            Pseudo Genes (incomplete)         :: 505 of 720
            Pseudo Genes (internal stop)      :: 128 of 720
            Pseudo Genes (multiple problems)  :: 123 of 720
            Pseudo Genes (short protein)      :: 3 of 720
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP046290.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
FEATURES             Location/Qualifiers
     source          1..2557
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_715"
                     /isolation_source="clinical isolate"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_715"
                     /db_xref="taxon:624"
                     /plasmid="unnamed5"
                     /geo_loc_name="Nigeria: Ibadan"
                     /collected_by="University of Ibadan"
     gene            <1..153
                     /locus_tag="FOC23_RS26225"
     CDS             <1..153
                     /locus_tag="FOC23_RS26225"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001318243.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_242412528.1"
                     /translation="PPVQPDRCALSGNYRLESNPVRHELSPLAAATDNRIRGVRLEVMR
                     LLRLN"
                     /name="replication initiation protein"
     gene            532..1155
                     /locus_tag="FOC23_RS25540"
                     /old_locus_tag="FOC23_25505"
     CDS             532..1155
                     /locus_tag="FOC23_RS25540"
                     /old_locus_tag="FOC23_25505"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="putative adhesin"
                     /protein_id="WP_226342037.1"
                     /translation="MDVTSHRRLFQKDGIGLSQTGKATQLVIMSHGGWKEISHPQTLFT
                     RQKGDGWTVVPKNLRIDFYTKDNDFTKGLSVLSEVNKRHTEAQKGLTPSLNISKDDLKV
                     LANARNIPQSKLEEEMMSQAIYRKEYATSNEKIKNYALYYHEQAQNIIQRHQDGLGNKN
                     IDIAFITDKNHKKHLSDIFKVINESGVKYDVIHFGACRVNREEK"
                     /name="putative adhesin"
     gene            complement(1381..1704)
                     /gene="mobA"
                     /locus_tag="FOC23_RS25545"
                     /old_locus_tag="FOC23_25510"
     CDS             complement(1381..1704)
                     /gene="mobA"
                     /locus_tag="FOC23_RS25545"
                     /old_locus_tag="FOC23_25510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_004988908.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKNVNSLTDDRVLKEVMRLGALQKKLFIDGKRIGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            1990..2184
                     /locus_tag="FOC23_RS25550"
                     /old_locus_tag="FOC23_25515"
     CDS             1990..2184
                     /locus_tag="FOC23_RS25550"
                     /old_locus_tag="FOC23_25515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_039059175.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHEIA
                     EELQNSIQTRFEAESGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(1714..1952)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.72e-122"
     Typing          complement(1385..1704)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="5.37e-62"
ORIGIN
        1 ccccccgttc agcccgaccg ctgcgcctta tccggtaact atcgtcttga gtccaacccg
       61 gtaagacacg aattatcgcc actggcagca gccactgata accgaattag aggagtaaga
      121 cttgaagtca tgcgcctgtt aaggctaaac tgaaagaaca agttttggtg actgcgctcc
      181 tccaagccag ttacctcggc tcaaagagtt ggtagctctg agaaccttcg aaaaaccgcc
      241 ttgcagggcg gttttttcgt ttacaggcag cagattactc gcagaaaaaa aggatctcaa
      301 gaagaacctt taattttttt tcacacttgg tatcctactt taacccataa aataaacact
      361 tacaccgaca cacccttaaa caaaagaaaa aaaacaataa aaaacaccgc aaaaatggat
      421 tgttaacaaa tgaaaatact caattcgaat ctcataacaa acatatcatc aacaataaga
      481 aatcaccttc taacatcatc caaaaatata aaaacacacc catcaccaaa catggacgta
      541 acaagtcatc gtcgtttatt ccagaaagac ggaataggat tgagccaaac aggaaaagca
      601 acacaacttg tcattatgtc gcatggtgga tggaaagaga tctcccatcc acaaacacta
      661 ttcacgcgtc aaaaaggcga tggatggact gtagtcccca aaaacctaag aattgatttt
      721 tatacaaaag acaacgactt cacaaaggga ctaagcgttc tttcagaggt aaacaaacgc
      781 catactgaag ctcaaaaagg gttaacacca tcactaaaca taagcaaaga tgacctaaaa
      841 gttctagcga acgcgcgcaa tatacctcaa tcaaaattag aagaagaaat gatgtcacaa
      901 gccatatata gaaaagaata cgcaacaagt aatgagaaga taaaaaacta tgctctatat
      961 taccatgaac aagcccaaaa tattatacaa agacatcaag atggcttagg aaacaaaaat
     1021 attgatatag catttataac tgataaaaat cataagaagc acctttctga catatttaaa
     1081 gtaataaatg aatcaggagt aaaatatgat gtaattcact ttggcgcttg ccgagtaaat
     1141 agagaggaga aataatcatc atttaccata atcccttaat tgtacgcacc actgaaacgc
     1201 gctgaacgcg attctgacgc agacaccaca aaaatagatg ttttaccccg gaaaaacagg
     1261 aaggatgcgt caggatcgtt ttcagctcgc tgcatagcta tgcatgaaag cgaatggaga
     1321 tcactttggg agcttaccgt gttcataccg tctgttttca acagttttct ccccgggaag
     1381 ctaatctgcc ataagcctgg ataacagggc acggtgatac tccgtaatag cgatcagcac
     1441 ctccgcatac tccctgtccc cgatacgctt gccgtcgata aagagttttt tctgtaacgc
     1501 ccccagtctc ataacttctt tcagcacccg atcatcagtc agtgagttaa cgttcttacc
     1561 gagagctgcc gcccgtaaaa aaccagaaac ggtcttgccg cattcagcag ccctttttct
     1621 gatttcctgg tcttcttctg ccgtcagacg aacagggcga ctgatagccc gcctgcgcgt
     1681 attacttcca cttcgttttg tcataaaaca tggctccgta tctgacacgg ggtgtcgggg
     1741 cgaagccctg accagggtaa ttgtaatagc gtgcatgtat gcgcggtata acaattacac
     1801 atcctgtcct gtcagcaagt tcgaattacc gacaaaggca cggcagtttt tttggcagtg
     1861 acagtattgt caggcagaaa tacccgtcaa tgcgtcagac ggcagaatac cggcggtaaa
     1921 acagtcgaaa agtggtacgc gatataatca cacaacgcag atgacagaca gaacggagaa
     1981 aacagaaaga tgaacaagca gcagcaaacc gtactcaaca tggcgggatt cataaaaagc
     2041 cagagcctga cgctgctcga aaagctggac gcactcgatg ccgacgaaca ggccgccatg
     2101 tgtgagaagc tgcacgaaat cgcggaagaa ctccagaaca gcatacagac acgctttgaa
     2161 gcggaaagtg gcaccggggt ataacagtgt atcctgctcc agacaggatg cagaacggta
     2221 taccggtgcg taaggagaaa atgtcacata aggcgctctt ccgcttcctc gctcactgac
     2281 tcgctacgct cggtcgttcg actgcggcga gcggtgtcag ctcactcaaa ggcggtaatg
     2341 cggttatcca cagaatcagg ggataacgcc ggaaagaaca tgtgagcaaa aagccgaagg
     2401 cagggacaaa ggccgcgcag gtggcgtttt tccataggct ccgcccccct gacgagcatc
     2461 acaaaaatcg acgctcaagt cagaggtggc gaaacccgac aggactataa agataccagg
     2521 cgtttccccc tggaagctcc ctcgtgcgct ctcctgt
//
